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| -rw-r--r-- | README.md | 17 |
1 files changed, 15 insertions, 2 deletions
@@ -14,7 +14,7 @@ guix environment --load=guix.scm Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash -env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm +env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --expose=$HOME/genotype_files/ --load=guix.scm python3 import redis ``` @@ -22,7 +22,7 @@ python3 Better run a proper container ``` -env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm +env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose=$HOME/genotype_files/ --load=guix.scm ``` If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception: @@ -121,6 +121,19 @@ pip freeze --path venv/lib/python3.8/site-packages > requirements.txt ``` +## Genotype Files + +You can get the genotype files from http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL and save them on your host machine at, say `$HOME/genotype_files` with something like: + +```bash +$ mkdir -p $HOME/genotype_files +$ cd $HOME/genotype_files +$ yes | 7z x genotype_files.tar.7z +$ tar xf genotype_files.tar +``` + +The `genotype_files.tar.7z` file seems to only contain the **BXD.geno** genotype file. + ## QTLReaper (rust-qtlreaper) and Trait Files To run QTL computations, this system makes use of the [rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) utility. |